DB code: D00111

RLCP classification 3.103.69900.359 : Transfer
CATH domain 3.40.50.450 : Rossmann fold Catalytic domain
3.40.50.460 : Rossmann fold Catalytic domain
E.C. 2.7.1.11
CSA 1pfk
M-CSA 1pfk
MACiE

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam RefSeq
P00512 6-phosphofructokinase
Phosphofructokinase
EC 2.7.1.11
Phosphohexokinase
PF00365 (PFK)
[Graphical View]
P0A796 6-phosphofructokinase isozyme 1
EC 2.7.1.11
6-phosphofructokinase isozyme I
Phosphofructokinase 1
Phosphohexokinase 1
PF00365 (PFK)
[Graphical View] 		NP_418351.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_491535.1 (Protein)
NC_007779.1 (DNA/RNA sequence)

KEGG enzyme name
6-phosphofructokinase
phosphohexokinase
phosphofructokinase I
phosphofructokinase (phosphorylating)
6-phosphofructose 1-kinase
ATP-dependent phosphofructokinase
D-fructose-6-phosphate 1-phosphotransferase
fructose 6-phosphate kinase
fructose 6-phosphokinase
nucleotide triphosphate-dependent phosphofructokinase
phospho-1,6-fructokinase
PFK

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P00512 K6PF_BACST ATP + D-fructose 6-phosphate = ADP + D- fructose 1,6-bisphosphate. Homotetramer. Cytoplasm.
P0A796 K6PF1_ECOLI ATP + D-fructose 6-phosphate = ADP + D- fructose 1,6-bisphosphate. Homotetramer. Cytoplasm.

KEGG Pathways
Map code Pathways E.C.
MAP00010 Glycolysis / Gluconeogenesis
MAP00030 Pentose phosphate pathway
MAP00051 Fructose and mannose metabolism
MAP00052 Galactose metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00002 C00085 C00008 C00354
E.C.
Compound Magnesium ATP D-Fructose 6-phosphate ADP D-Fructose 1,6-bisphosphate
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide carbohydrate,phosphate group/phosphate ion amine group,nucleotide carbohydrate,phosphate group/phosphate ion
ChEBI 18420
 18420
 		15422
 15422
 		61553
 61553
 		16761
 16761
 		37736
 37736
PubChem 888
 888
 		5957
 5957
 		439160
 439160
 		6022
 6022
 		172313
 172313
1pfkA01 Bound:_MG_325 Unbound Unbound Bound:ADP_324 Bound:FBP
1pfkB01 Bound:_MG_325 Unbound Unbound Bound:ADP_324 Bound:FBP
2pfkA01 Unbound Unbound Unbound Unbound Unbound
2pfkB01 Unbound Unbound Unbound Unbound Unbound
2pfkC01 Unbound Unbound Unbound Unbound Unbound
2pfkD01 Unbound Unbound Unbound Unbound Unbound
3pfkA01 Unbound Unbound Unbound Unbound Unbound
4pfkA01 Bound:_MG_325 Unbound Bound:F6P Bound:ADP_324 Unbound
6pfkA01 Unbound Unbound Unbound Unbound Unbound
6pfkB01 Unbound Unbound Unbound Unbound Unbound
6pfkC01 Unbound Unbound Unbound Unbound Unbound
6pfkD01 Unbound Unbound Unbound Unbound Unbound
1mtoA01 Unbound Unbound Bound:F6P Unbound Unbound
1mtoB01 Unbound Unbound Bound:F6P Unbound Unbound
1mtoC01 Unbound Unbound Bound:F6P Unbound Unbound
1mtoD01 Unbound Unbound Bound:F6P Unbound Unbound
1mtoE01 Unbound Unbound Bound:F6P Unbound Unbound
1mtoF01 Unbound Unbound Bound:F6P Unbound Unbound
1mtoG01 Unbound Unbound Bound:F6P Unbound Unbound
1mtoH01 Unbound Unbound Bound:F6P Unbound Unbound
1pfkA02 Unbound Unbound Unbound Unbound Bound:FBP
1pfkB02 Unbound Unbound Unbound Unbound Bound:FBP
2pfkA02 Unbound Unbound Unbound Unbound Unbound
2pfkB02 Unbound Unbound Unbound Unbound Unbound
2pfkC02 Unbound Unbound Unbound Unbound Unbound
2pfkD02 Unbound Unbound Unbound Unbound Unbound
3pfkA02 Unbound Unbound Unbound Unbound Unbound
4pfkA02 Unbound Unbound Unbound Unbound Unbound
6pfkA02 Unbound Unbound Unbound Unbound Unbound
6pfkB02 Unbound Unbound Unbound Unbound Unbound
6pfkC02 Unbound Unbound Unbound Unbound Unbound
6pfkD02 Unbound Unbound Unbound Unbound Unbound
1mtoA02 Unbound Unbound Unbound Unbound Unbound
1mtoB02 Unbound Unbound Unbound Unbound Unbound
1mtoC02 Unbound Unbound Unbound Unbound Unbound
1mtoD02 Unbound Unbound Unbound Unbound Unbound
1mtoE02 Unbound Unbound Unbound Unbound Unbound
1mtoF02 Unbound Unbound Unbound Unbound Unbound
1mtoG02 Unbound Unbound Unbound Unbound Unbound
1mtoH02 Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot & literature [7] & [11]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1pfkA01 ARG 72;THR 125;ASP 127;ASP 129 ASP 103;ASP 129(Magnesium binding) GLY 11
1pfkB01 ARG 72;THR 125;ASP 127;ASP 129 ASP 103;ASP 129(Magnesium binding) GLY 11
2pfkA01 ARG 72;THR 125;ASP 127;ASP 129 ASP 103;ASP 129(Magnesium binding) GLY 11
2pfkB01 ARG 72;THR 125;ASP 127;ASP 129 ASP 103;ASP 129(Magnesium binding) GLY 11
2pfkC01 ARG 72;THR 125;ASP 127;ASP 129 ASP 103;ASP 129(Magnesium binding) GLY 11
2pfkD01 ARG 72;THR 125;ASP 127;ASP 129 ASP 103;ASP 129(Magnesium binding) GLY 11
3pfkA01 ARG 72;THR 125;ASP 127;ASP 129 ASP 103;ASP 129(Magnesium binding) GLY 11
4pfkA01 ARG 72;THR 125;ASP 127;ASP 129 ASP 103;ASP 129(Magnesium binding) GLY 11
6pfkA01 ARG 72;THR 125;ASP 127;ASP 129 ASP 103;ASP 129(Magnesium binding) GLY 11
6pfkB01 ARG 72;THR 125;ASP 127;ASP 129 ASP 103;ASP 129(Magnesium binding) GLY 11
6pfkC01 ARG 72;THR 125;ASP 127;ASP 129 ASP 103;ASP 129(Magnesium binding) GLY 11
6pfkD01 ARG 72;THR 125;ASP 127;ASP 129 ASP 103;ASP 129(Magnesium binding) GLY 11
1mtoA01 ARG 72;THR 125;ASP 127;ASP 129 ASP 103;ASP 129(Magnesium binding) GLY 11
1mtoB01 ARG 72;THR 125;ASP 127;ASP 129 ASP 103;ASP 129(Magnesium binding) GLY 11
1mtoC01 ARG 72;THR 125;ASP 127;ASP 129 ASP 103;ASP 129(Magnesium binding) GLY 11
1mtoD01 ARG 72;THR 125;ASP 127;ASP 129 ASP 103;ASP 129(Magnesium binding) GLY 11
1mtoE01 ARG 72;THR 125;ASP 127;ASP 129 ASP 103;ASP 129(Magnesium binding) GLY 11
1mtoF01 ARG 72;THR 125;ASP 127;ASP 129 ASP 103;ASP 129(Magnesium binding) GLY 11
1mtoG01 ARG 72;THR 125;ASP 127;ASP 129 ASP 103;ASP 129(Magnesium binding) GLY 11
1mtoH01 ARG 72;THR 125;ASP 127;ASP 129 ASP 103;ASP 129(Magnesium binding) GLY 11
1pfkA02 ARG 171
1pfkB02 ARG 171
2pfkA02 ARG 171
2pfkB02 ARG 171
2pfkC02 ARG 171
2pfkD02 ARG 171
3pfkA02 ARG 171
4pfkA02 ARG 171
6pfkA02 ARG 171
6pfkB02 ARG 171
6pfkC02 ARG 171
6pfkD02 ARG 171
1mtoA02 ARG 171
1mtoB02 ARG 171
1mtoC02 ARG 171
1mtoD02 ARG 171
1mtoE02 ARG 171
1mtoF02 ARG 171
1mtoG02 ARG 171
1mtoH02 ARG 171

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
p.58-60
[7]
p.984-986, p.992
[10]
[11]

References
[1]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
Medline ID 79199719
PubMed ID 156307
Journal Nature
Year 1979
Volume 279
Pages 500-4
Authors Evans PR, Hudson PJ
Title Structure and control of phosphofructokinase from Bacillus stearothermophilus.
Related PDB
Related UniProtKB P00512
[2]
Resource
Comments
Medline ID
PubMed ID 6462132
Journal Biochem J
Year 1981
Volume 199
Pages 427-32
Authors Jarvest RL, Lowe G, Potter BV
Title The stereochemical course of phosphoryl transfer catalysed by Bacillus stearothermophilus and rabbit skeletal-muscle phosphofructokinase with a chiral [16O,17O,18O]phosphate ester.
Related PDB
Related UniProtKB
[3]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 6115424
Journal Philos Trans R Soc Lond B Biol Sci
Year 1981
Volume 293
Pages 53-62
Authors Evans PR, Farrants GW, Hudson PJ
Title Phosphofructokinase: structure and control.
Related PDB 3pfk 4pfk
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 6115426
Journal Philos Trans R Soc Lond B Biol Sci
Year 1981
Volume 293
Pages 75-92
Authors Lowe G, Cullis PM, Jarvest RL, Potter BV, Sproat BS
Title Stereochemistry of phosphoryl transfer.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 2949086
Journal J Mol Biol
Year 1986
Volume 191
Pages 713-20
Authors Evans PR, Farrants GW, Lawrence MC
Title Crystallographic structure of allosterically inhibited phosphofructokinase at 7 A resolution.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 2952886
Journal Nature
Year 1987
Volume 326
Pages 811-2
Authors Lau FT, Fersht AR
Title Conversion of allosteric inhibition to activation in phosphofructokinase by protein engineering.
Related PDB
Related UniProtKB
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).
Medline ID 89125622
PubMed ID 2975709
Journal J Mol Biol
Year 1988
Volume 204
Pages 973-94
Authors Shirakihara Y, Evans PR
Title Crystal structure of the complex of phosphofructokinase from Escherichia coli with its reaction products.
Related PDB 1pfk
Related UniProtKB P0A796
[8]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 2527305
Journal J Mol Biol
Year 1989
Volume 207
Pages 805-21
Authors Rypniewski WR, Evans PR
Title Crystal structure of unliganded phosphofructokinase from Escherichia coli.
Related PDB 2pfk
Related UniProtKB
[9]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 2136935
Journal Nature
Year 1990
Volume 343
Pages 140-5
Authors Schirmer T, Evans PR
Title Structural basis of the allosteric behaviour of phosphofructokinase.
Related PDB 6pfk
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 1386803
Journal Eur J Biochem
Year 1992
Volume 207
Pages 1109-14
Authors Laine R, Deville-Bonne D, Auzat I, Garel JR
Title Interaction between the carboxyl groups of Asp127 and Asp129 in the active site of Escherichia coli phosphofructokinase.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 1304907
Journal Protein Sci
Year 1992
Volume 1
Pages 254-8
Authors Auzat I, Garel JR
Title pH dependence of the reverse reaction catalyzed by phosphofructokinase I from Escherichia coli: implications for the role of Asp 127.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 7876126
Journal J Biol Chem
Year 1995
Volume 270
Pages 3828-35
Authors Byrnes WM, Hu W, Younathan ES, Chang SH
Title A chimeric bacterial phosphofructokinase exhibits cooperativity in the absence of heterotropic regulation.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 7783204
Journal J Mol Biol
Year 1995
Volume 249
Pages 478-92
Authors Auzat I, Gawlita E, Garel JR
Title Slow ligand-induced transitions in the allosteric phosphofructokinase from Escherichia coli.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 7869376
Journal J Mol Biol
Year 1995
Volume 246
Pages 248-53
Authors Auzat I, Le Bras G, Garel JR
Title Hypercooperativity induced by interface mutations in the phosphofructokinase from Escherichia coli.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 11976749
Journal Arch Microbiol
Year 2002
Volume 177
Pages 401-9
Authors Hansen T, Musfeldt M, Schonheit P
Title ATP-dependent 6-phosphofructokinase from the hyperthermophilic bacterium Thermotoga maritima: characterization of an extremely thermophilic, allosterically regulated enzyme.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 12390023
Journal Biochemistry
Year 2002
Volume 41
Pages 12967-74
Authors Riley-Lovingshimer MR, Ronning DR, Sacchettini JC, Reinhart GD
Title Reversible ligand-induced dissociation of a tryptophan-shift mutant of phosphofructokinase from Bacillus stearothermophilus.
Related PDB 1mto
Related UniProtKB

Comments
This enzyme contains two binding sites for ADP-Mg2+; one is the active site between the two domains, and the other is effector site in the smaller subunit. Moreover, this enzyme has two conformational states, R- and T-states, by allosteric behavior (see [9]).
According to the literature [7], [10] & [11], the reaction proceeds as follows:
(1) Asp127 acts as a general base, whose pKa seems to be modulated by Asp129, to deprotonate the acceptor group, 1-OH of Fructose 6-phosphate (F6P). Asp129 is also involved indirectly in binding of the cofactor magnesium ion, through water molecules.
(2) The activated acceptor group makes a nucleophilic attack on the gamma-phosphate of ATP.
(3) The pentacovalent phosphoryl group is stabilized by Arg171, Arg72, Thr125 and mainchain amide of Gly11, along with the magnesium ion bound to Asp103. The magnesium ion bridges gamma- and beta-phosphate groups.

Created Updated
2004-10-15 2009-02-26